[gmx-users] Increase temperature to 550K
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 11 16:24:05 CET 2009
Chih-Ying Lin wrote:
> The system = one lysozyme + TIP3P water
> I was put the system in NTP simulation.
> Under 550K, all water molecules should evaporate entirely , I suppose ???
Is this what you want to happen? Are the force field parameters appropriate for
>>From Justin =>
> "There are plenty of other methodological concerns (pressure
> coupling especially) "
> Would you please direct me about this ?
Yes, search the literature. As I said, a number of groups have been doing
high-temperature MD for a long time; there are papers out there with methodology
you might be able to follow, but since you have not described your goals (are
you trying to super-heat a lysozyme solution? improve sampling?) then there is
nothing specific to offer.
> Thank you
> I agree with Mark's earlier comment; the water model alone is not the most
> immediate concern. A colleague of mine is currently doing lots of
> high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER
> force fields. There are plenty of other methodological concerns (pressure
> coupling especially); a thorough search of the literature will give you some
> insights into what might be wrong. Plenty of groups have successfully been
> doing high-temperature MD for a number of years.
> Chih-Ying Lin wrote:
>> the water model is TIP3P.
>> I think the problem is hidden in your water force field model.
>> > The simulation system is merely water + one lysozyme.
>> > I increase temperate to 550K.
>> > Then, the simulation broke.
>> > The following message is shown.
>> > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0)
>> > mpiexec: Warning: task 0 exited with status 1.
>> > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed).
>> > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault).
>> > Anything wrong with the simulation?
>> > Thank you
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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